Ultra-sensitive detection of transposon insertions in multiple families by transposable element display sequencing

Mobilization of transposable elements (TEs) can generate large-effect mutations. However, because novel TE insertions are difficult to detect and transposition is generally rare, the true rate and landscape of novel insertions remains unexplored for most TEs. Here, we present a TE display sequencing approach that leverages targeted amplification of TE ends to detect unreferenced TE insertions with high sensitivity and specificity. By implementing this approach on serial dilutions of genomic DNA from A. thaliana lines carrying different repertoires of novel TE insertions, we show that the method can detect TE insertions present at frequencies as low as 1:250,000 in a DNA sample. Additionally, TE display sequencing can be multiplexed to simultaneously detect insertions for distinct TE families, including retrotransposons and DNA transposons, increasing its versatility and cost-effectiveness for studying complex mobilomes. Importantly, when combined with nanopore sequencing, this approach enables the identification of insertions using long reads and achieves a turnaround time from DNA extraction to insertion identification of less than 24 hours, significantly reducing the time to response. Analysis of TE insertions in large populations of A. thaliana plants undergoing a transposition burst demonstrates the power of multiplex TE display sequencing to assess the rates and allele frequencies of heritable insertions, enabling its implementation to study large-scale evolution and resequencing experiments. Furthermore, we found that approximately 6% of de novo TE insertions exhibit recurrent allele frequency changes consistent with positive or negative selection. We conclude that TE display sequencing is an ultra-sensitive, specific, rapid, and cost-effective approach to study the rate and landscape of novel insertions for multiple TEs in large-scale population experiments. We provide a step-by-step experimental protocol as well as ready-to-use bioinformatics pipelines, ensuring straightforward implementation of the method.